To begin, I have written an enormous discussion of homebrew class design for 3.5. It focuses a considerable amount of attention on prestige classes. I stand by every word in it for Pathfinder as well as 3.5. I consider that answer, more than this one, to be the answer you want to read.
But I do want to address Pathfinder specifically:
For Pathfinder specifically, you have to consider whether or not you would like to continue Paizo’s trend of downplaying prestige classes. Personally, I feel like they were overcompensating for any issues 3.5 had in this regard, and made prestige classes too small a part of the game. Your mileage may vary; lots of people love the fact that almost no one in Pathfinder uses prestige classes.
If you do go that route, I recommend doing so by making small prestige classes – three- and five-level deals that you can hop into for a neat, unusual trick, without taking too much away from your base class. I made similar recommendations for 3.5, but in that case it was mostly because I wanted to countermand the tendency in 3.5 to favor ten-level prestige classes even when it wasn’t warranted; ten-level prestige classes certainly can be a good idea in 3.5, you just need to make a class that deserves it.
In Pathfinder, that’s still true, but by the precedent set by other Pathfinder material, you shouldn’t make ten-level prestige classes. Yes, I know Paizo has: I would consider that a mistake in light of their desire to down-play prestige classes. Instead, they just made the prestige classes simply not that great, or too painful to take because of how a diversion from your base class affected you. I consider that less than ideal. Instead, just make smaller prestige classes.
Small prestige classes don’t have to be small in concept; in fact, being small gives you freedom to be really specific and detailed. It means less work per prestige class, and fewer demands on characters’ levels, which means they are more likely to be able to afford those levels for some niche thing.
On the other hand, you can reject that Pathfinder paradigm, and return to 3.5-esque prestige classes, where they are significant and important, and it is often less a matter of if you will prestige class, but when and in which. If you decide to go that route, my 3.5 advice fits perfectly.
One would think any good (and frankly even many Neutral) gods would have a place for opposition of black magic and foul sorcery. That's kinda like saying "who doesn't like murderers?" "Anyone but Norgorberites I guess?" is the answer. Even CN churches won't like it if there's enslaving/domination going on from the baddies.
Good type gods that are the most martial are Iomedae and Sarenrae. Gods with more of a craftsman aspect that might be Black Powder friendly are Torag and Abadar.
You'd do better to include what AP you're playing in and what kind of character you'd like to be like beyond the class details to get a more helpful answer. What part of Golarion? What kind of bad guys? If the answer is "necromancers" then suddenly Pharasma jumps up pretty highly in the choices, for example.
If you'd like a "Conan the savage who doesn't like arcane magic" feel, then the Kellid race and Gorum as a deity makes a lot of sense. Kellids from Numeria get some gun contact and would work very well for Reign of Winter (they hate White Witches), Iron Gods (from the area), and Wrath of the Righteous (from the area).
Best Answer
If your goal is to make your created deities fit in with the existing deity mechanics and/or the existing Pathfinder deity style as much as possible, then I would highly recommend getting the Gods and Magic book by Sean Reynolds. This is a Paizo campaign setting guide for the official Pathfinder setting, but the PDF is only $13 USD and contains a ton of detail on the existing deities in Pathfinder:
By comparison you should be able to construct your own with as much or as little detail necessary for your campaign.